Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/ensembl/ctat_ref_annot.interval_list
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/276a5b7cb5469752b9f3101f7406de/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/276a5b7cb5469752b9f3101f7406de/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/8940e2b917761cb948451fca89e0f4/rna_s1200_S21.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/ensembl/ref_annot.gtf.refflat
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/46199de6db590afebdc3d82bc19c9e/rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (6 inputs)
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
May 27, 2026 4:05:01 PM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.0-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed May 27 16:05:01 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT rna_s1200_S21.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1200_S21_rna_metrics.txt --TMP_DIR ./tmp --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Wed May 27 16:05:01 GMT 2026] Executing as ?@nf-21276a5b7cb5469752b9f3101f7406de-70f4d-lspwk on Linux 6.12.83 amd64; OpenJDK 64-Bit Server VM 20-internal-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.1.0
INFO 2026-05-27 16:05:03 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-27 16:05:20 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 16s. Last read position: chr1:111,230,487
INFO 2026-05-27 16:05:32 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 12s. Last read position: chr1:233,139,804
INFO 2026-05-27 16:05:51 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 19s. Last read position: chr2:177,215,659
INFO 2026-05-27 16:06:20 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 29s. Last read position: chr3:53,864,996
INFO 2026-05-27 16:06:42 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 21s. Last read position: chr4:143,538,860
INFO 2026-05-27 16:07:05 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 22s. Last read position: chr5:181,237,672
INFO 2026-05-27 16:07:12 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 6s. Last read position: chr6:43,499,011
INFO 2026-05-27 16:07:35 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 23s. Last read position: chr7:44,696,070
INFO 2026-05-27 16:07:54 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 18s. Last read position: chr8:100,706,769
INFO 2026-05-27 16:08:14 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 20s. Last read position: chr9:136,454,161
INFO 2026-05-27 16:08:29 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 15s. Last read position: chr11:46,547,131
INFO 2026-05-27 16:08:48 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 19s. Last read position: chr12:8,605,335
INFO 2026-05-27 16:09:10 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 21s. Last read position: chr12:124,911,968
INFO 2026-05-27 16:09:41 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 30s. Last read position: chr15:34,904,443
INFO 2026-05-27 16:09:56 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 15s. Last read position: chr16:22,513,880
INFO 2026-05-27 16:10:13 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 17s. Last read position: chr17:7,311,406
INFO 2026-05-27 16:10:27 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 13s. Last read position: chr17:76,047,903
INFO 2026-05-27 16:10:41 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 14s. Last read position: chr19:10,689,198
INFO 2026-05-27 16:10:54 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 12s. Last read position: chr20:3,755,548
INFO 2026-05-27 16:11:09 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 15s. Last read position: chr22:36,518,625
INFO 2026-05-27 16:11:23 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 13s. Last read position: chrX:154,360,515
[Wed May 27 16:11:28 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 6.45 minutes.
Runtime.totalMemory()=2430074880